Methods and apparatus for electron or positron capture dissociation

ABSTRACT

The present invention relates to mass spectrometers capable of performing electron (or positron) capture dissociation, methods of performing tandem mass spectrometry, methods of performing electron capture dissociation, and methods of performing positron capture dissociation. In one embodiment, a mass spectrometer capable of performing electron or positron capture dissociation is provided that comprises a first mass analyzer, a magnetic trap downstream of the first mass analyzer, a second mass analyzer downstream of the magnetic trap, and an electron or positron source positioned such that electrons or positrons may be supplied to the magnetic trap.

FIELD OF THE INVENTION

The present invention generally relates to methods of performingelectron or positron capture dissociation and to mass spectrometerscapable of performing electron or positron capture dissociation.

BACKGROUND OF THE INVENTION

Mass spectrometry allows the determination of the mass-to-charge ratio(m/z) of ions of sample molecules. Mass spectrometry involves ionizingthe sample molecule or molecules and then analyzing the ions in ananalyzer that has a detector. Various mass spectrometers are known.

Tandem mass spectrometry involves ionization of a sample into ions,which are introduced into a mass analyzer. The mass analyzer selectsparent ions of a desired m/z for further analysis. The parent ions arethen fragmented by one or more of a variety of methods into productions. The product ions are then analyzed by a mass analyzer to determinethe mass-to-charge ratios of the product ions and thus obtain a massspectrum of the product ions. Tandem mass spectrometry has becomeincreasingly important for the analysis of bio-molecules such aspeptides and proteins, and enables the determination of amino acidsequence of peptides and proteins.

Fragmentation of parent ions is typically accomplished usingcollision-induced dissociation (CID), which involves colliding theparent ions with gas atoms or molecules in order to fragment the parentions. Other methods of fragmenting parent ions are known, such as, forexample, electron capture dissociation (ECD). Electron capturedissociation involves the capture of low energy electrons by ions, whichleads to the subsequent fragmentation of the ions. Electron capturedissociation produces cleavage patterns of polypeptides that aredifferent than cleavage patterns of polypeptides produced by CID, andthe nature of the cleavage patterns makes ECD a desirable fragmentationmethod for analysis of peptides and proteins by tandem mass spectrometry(see, e.g., Kruger et al., Electron capture dissociation of multiplycharged peptide cations, International Journal of Mass Spectrometry,185–187, 787–793 (1999); Kruger et al., Electron capture versusenergetic dissociation of protein ions, International Journal of MassSpectrometry, 182–183, 1–5 (1999); Zubarev et al., Electron CaptureDissociation of Multiply Charged Protein Cations. A Nonergodic Process,J. Am. Chem. Soc., 120, 3265–3266 (1998); and Zubarev et al., ElectronCapture Dissociation for Structural Characterization of Multiply ChargedProtein Cations, Anal. Chem., 72, 563–573 (2000)).

Electron capture dissociation is typically performed using a Fouriertransform ion cyclotron resonance (FT-ICR) mass spectrometer. Electroncapture dissociation is performed in such an instrument by trappingparent ions in the FT-ICR cell and reacting the trapped ions withelectrons that are injected into the cell. The product ions that resultare also mass analyzed using the FT-ICR cell. Although analysis ofpeptides and proteins by tandem mass spectrometry using ECD forfragmentation is desirable, the use of ECD has been limited due to boththe large size and the expense of FT-ICR mass spectrometers.

SUMMARY OF THE INVENTION

The present invention generally relates to methods of performingelectron or positron capture dissociation and to mass spectrometerscapable of performing electron or positron capture dissociation. In oneaspect of the invention, a mass spectrometer is provided that comprisesa first mass analyzer, a magnetic trap downstream of the first massanalyzer, a second mass analyzer downstream of the magnetic trap, and anelectron or positron source positioned such that electrons or positronsmay be supplied to the magnetic trap.

In another aspect of the invention, a method of performing electroncapture dissociation of ions is provided. The method comprises (a)generating electrons using an electron source, (b) confining theelectrons to a region within a magnetic trap, and (c) injecting positiveions into the magnetic trap such that electron capture dissociation ofat least some of the ions occurs.

In yet another aspect of the invention, a method of performing positroncapture dissociation of ions is also provided. The method comprises (a)generating positrons using a positron source, (b) confining thepositrons to a region within a magnetic trap, and (c) injecting negativeions into the magnetic trap such that positron capture dissociation ofat least some of the ions occurs.

Various methods of performing tandem mass spectrometry using a massspectrometer comprising a first mass analyzer, a magnetic trap, and asecond mass analyzer are provided. One method comprises (a) generatingpositive sample ions using an ion source, (b) injecting the sample ionsinto the first mass analyzer, (c) using the first mass analyzer,selecting parent ions from the sample ions to be subjected to electroncapture dissociation, (d) injecting the parent ions into the magnetictrap for reaction with electrons confined in the magnetic trap such thatelectron capture dissociation of at least some of the parent ions occursto produce product ions, (e) ejecting the product ions from the magnetictrap into the second mass analyzer, and (f) detecting the product ionsusing the second mass analyzer. Another method comprises (a) generatingnegative sample ions using an ion source, (b) injecting the sample ionsinto the first mass analyzer, (c) using the first mass analyzer,selecting parent ions from the sample ions to be subjected to positroncapture dissociation, (d) injecting the parent ions into the magnetictrap for reaction with positrons confined in the magnetic trap such thatpositron capture dissociation of at least some of the parent ions occursto produce product ions, (e) ejecting the product ions from the magnetictrap into the second mass analyzer, and (f) detecting the product ionsusing the second mass analyzer.

Yet another method of performing tandem mass spectrometry using a massspectrometer comprising a first mass analyzer, a magnetic trap, and asecond mass analyzer comprises (a) generating positive sample ions usingan ion source, (b) injecting the sample ions into the first massanalyzer, (c) using the first mass analyzer, selecting parent ions fromthe sample ions to be subjected to electron capture dissociation, (d)injecting and confining the parent ions in the magnetic trap, (e)injecting electrons into the magnetic trap for reaction with theconfined parent ions such that electron capture dissociation of at leastsome of the parent ions occurs to produce product ions, (f) ejecting theproduct ions from the magnetic trap into the second mass analyzer, and(g) detecting the product ions using the second mass analyzer. A furthermethod comprises (a) generating negative sample ions using an ionsource, (b) injecting the sample ions into the first mass analyzer, (c)using the first mass analyzer, selecting parent ions from the sampleions to be subjected to positron capture dissociation, (d) injecting andconfining the parent ions in the magnetic trap, (e) injecting positronsinto the magnetic trap for reaction with the confined parent ions suchthat positron capture dissociation of at least some of the parent ionsoccurs to produce product ions, (f) ejecting the product ions from themagnetic trap into the second mass analyzer, and (g) detecting theproduct ions using the second mass analyzer.

In another aspect of the invention, a mass spectrometer is provided thatcomprises a first mass analyzer, a field-free region downstream from thefirst mass analyzer, an electron or positron source positioned such thatelectrons or positrons may be supplied to the field-free region, and asecond mass analyzer downstream of the field-free region.

In yet a further aspect of the invention, a method of performing tandemmass spectrometry using a mass spectrometer comprising a first massanalyzer, a field-free region, an electron source, and a second massanalyzer is provided. The method comprises (a) generating positivesample ions using an ion source, (b) injecting the sample ions into thefirst mass analyzer, (c) using the first mass analyzer, selecting parentions from the sample ions to be subjected to electron capturedissociation, (d) providing electrons in the field-free region using theelectron source, (e) injecting the parent ions into the field-freeregion such that electron capture dissociation of at least some of theproduct ions occurs and such that at least some of the product ions passinto the second mass analyzer, and (f) detecting the product ions usingthe second mass analyzer.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 illustrates one embodiment of a mass spectrometer according tothe present invention.

FIG. 2 illustrates another embodiment of a mass spectrometer accordingto the present invention.

FIG. 3 illustrates a further embodiment of a mass spectrometer accordingto the present invention.

FIG. 4 is a graph of Penning trap DC voltage (V₀) versus interactiontime of a parent ion having a mass-to-charge ratio of 1000. The graphalso illustrates the effect of Penning trap DC voltages on electrondensity in a Penning trap.

FIG. 5 is a graph of Penning trap DC voltage (V₀) versus reactionprobability of a parent ion with a mass-to-charge ratio of 1000.

FIG. 6 is a graph of kinetic energy of product ions versus ejectionefficiency of the product ions from the Penning trap. The thick dashedline represents ejection efficiency of the product ions when there is nofield in the Penning trap (i.e., B=0 and V₀=0). The thick solid linerepresents the ejection efficiency of the product ions when V₀=20 Volts(V) and B=0 Tesla (T). The thin lines represent the ejectionefficiencies of product ions of varying mass-to-charge ratios when B=1.3Tesla (T) and V₀=20 V.

FIG. 7 illustrates an embodiment of a mass spectrometer according to thepresent invention with a magnetic trap and mesh trapping electrodes.FIG. 7 also includes a graph of a possible electric potential along thez axis when both electrons and positive ions are confined in themagnetic trap of the mass spectrometer.

FIG. 8 illustrates an embodiment of a mass spectrometer according to thepresent invention with a field-free region.

FIG. 9 illustrates another embodiment of a mass spectrometer accordingto the present invention with a field-free region.

DETAILED DESCRIPTION OF THE INVENTION

The present invention relates to a mass spectrometer capable ofperforming electron (or positron) capture dissociation, methods ofperforming tandem mass spectrometry, methods of performing electroncapture dissociation, and methods of performing positron capturedissociation. Prior to describing this invention in further detail,however, the following terms will first be defined.

Definitions:

“Mass analyzer” means any device capable of sorting ions according totheir mass-to charge (m/z) ratios. Mass analyzers typically sort ionsusing electric and/or magnetic fields. Mass analyzers include, but arenot limited to, magnetic sectors, linear and three-dimensionalquadrupoles (including quadrupole mass filters and quadrupole iontraps), other multipole mass analyzers, Fourier transform ion cyclotronresonance mass spectrometers, and time-of-flight mass analyzers. Massanalyzers may include one or more detectors.

“Detector” means any device capable of detecting ions. Detectorsinclude, but are not limited to, Farady cups, channeltron detectors,electron multipliers, electron photomultipliers, array detectors, andmicrochannel plates.

“Magnetic trap” means a device having a “ring” electrode, two “end-cap”electrodes each having an opening for passage into the ring electrode,and magnets to produce a magnetic field. In order to trap chargedparticles, a magnetic trap uses a static electric field (typically aquadrupole field) applied between the end-cap electrodes and the ringelectrode to confine charged particles axially (i.e., in the zdirection, which is along a z axis between the openings of the end-capelectrodes) and a static magnetic field applied to confine chargedparticles radially (i.e., in the x and y directions perpendicular to thez axis). The “ring” electrode and the “end-cap” electrodes of a magnetictrap according to the present invention may be in any shape that allowstrapping of the desired particles. The magnets of a magnetic trap may beshaped and positioned in any manner that allows the required magneticfield to be applied to confine charged particles radially and allowcharged particles to enter and exit the ring electrode through theopenings in the end-cap electrodes. The magnets may be separate from theend-cap electrodes or the end-cap electrodes and the magnets may be oneand the same (i.e., magnetic end-cap electrodes). When magnetic end-capelectrodes are used, the magnetic trap uses a static electric fieldapplied between the end-cap electrodes and the ring electrode to confinecharged particles axially and a static magnetic field applied betweenthe magnetic end-cap electrodes to confine charged particles radially.As used herein, “magnetic trap” and “Penning trap” are synonymous.

“Ideal Penning trap” means a magnetic trap with hyperbolic end-cap andring electrodes where the ring electrode has a central inner radius ofr₀ and the end-cap electrodes are separated by a distance of √{squareroot over (2)}r₀. An ideal Penning trap has a uniform magnetic field (B)applied in the z direction (i.e., (0, 0, B)) and an ideal quadrupole DCpotential (ψ).

“Axial direction” or “z direction” means a direction along a “z axis”formed by the centers of the openings of the end-cap electrodes of amagnetic trap.

“Radial direction”, “x direction”, or “y direction” means a directionperpendicular to the “axial direction” or the “z axis” formed by thecenter of the openings of the end-cap electrodes of a magnetic trap.

“Parent ion” means, with respect to tandem mass spectrometry, the ion orions that is/are selected to be dissociated into fragments using amethod such as electron capture dissociation.

“Product ion” means, with respect to tandem mass spectrometry, the ionor ions that is/are produced from dissociating parent ions.

Electron (or positron) capture dissociation may be performed accordingto the present invention by confining electrons (or positrons) to aregion within a magnetic trap and injecting oppositely charged ions intothe magnetic trap such that electron (or positron) capture dissociationof at least some of the ions occurs via reaction of ions with theconfined electrons (or positrons). The oppositely charged ions arepreferably multiply charged ions (i.e., the ions preferably have acharge state of 2 or more).

In one aspect of the invention, a mass spectrometer capable ofperforming electron or positron capture dissociation is provided thatcomprises a first mass analyzer, a magnetic trap, and a second massanalyzer. The magnetic trap functions as an electron capturedissociation cell or as a positron capture dissociation cell duringoperation of the mass spectrometer. That is, the magnetic trap acts toconfine electrons or positrons for reaction with oppositely charged ionsthat are injected into the trap from one mass analyzer toward the othermass analyzer.

The first mass analyzer, magnetic trap, and second mass analyzer arearranged such that ions may move from the first mass analyzer to themagnetic trap and from the magnetic trap to the second mass analyzer.That is, the first mass analyzer, magnetic trap, and second massanalyzer are arranged in series (linear or otherwise). The massspectrometer may consist only of the first mass analyzer, the magnetictrap, and the second mass analyzer, or may include other elements (suchas, for example, one or more skimmers, ion guides, detectors, vacuumpumps, additional mass analyzers, etc.) before, after, between, and inaddition to the first mass analyzer, the magnetic trap, and the secondmass analyzer. As used herein, “downstream” means in a direction fromthe first mass analyzer to the magnetic trap to the second massanalyzer, and “upstream” means in a direction from the second massanalyzer to the magnetic trap to the first mass analyzer. As explainedbelow, appropriate DC and/or AC (e.g., RF) voltages and magnetic fieldsare applied to the mass analyzers and magnetic trap (using means forsupplying voltages and magnetic fields that are part of the massanalyzers, magnetic trap and/or mass spectrometer such as, for example,voltage supplies and magnets) in order to manipulate charged particlesin the mass spectrometer.

The magnetic trap includes permanent magnets or electromagnets that mayor may not be superconducting. In a preferred embodiment, the magnetsare permanent magnets. The magnetic field strength (B) of the magnetictrap is typically larger than 0.5 T, but may be of any field strengththat is sufficient for the particular embodiment.

The voltage range used with the first and second mass analyzers and themagnetic trap will depend on the particular analyzers and magnetic trapbeing used as well as the particular embodiment of the massspectrometer. For example, quadrupole and ion trap mass analyzers aretypically operated using voltages in the range of 1–100 eV while sectorsand time-of-flight mass analyzers are typically operated using voltagesin the range of 1–10 keV. The magnetic trap is typically operated in avoltage range of 1–100 eV. However, it should be noted that the massanalyzers and the magnetic trap may be operated using any voltage orvoltage range appropriate for the particular embodiment in which theyare being used.

The mass spectrometer typically includes an ion source to supply ions tothe first mass analyzer, although the ion source may be external to(i.e., not a part of) the mass spectrometer. Ions may be supplied usingion sources that use electrospray ionization (ESI), nanoelectrosprayionization (nESI), matrix assisted laser desorption ionization (MALDI),electron impact ionization (EI) or any other method for producing ions.The ion flow in the mass spectrometer is typically from an ion source tothe first mass analyzer, from the first mass analyzer to the magnetictrap, and from the magnetic trap to the second mass analyzer. In someembodiments, however, it may be desirable for ions to be directed fromthe second mass analyzer back through the magnetic trap to the firstmass analyzer and, if desired, again through the magnetic trap to thesecond mass analyzer. In some embodiments, ions may be passed throughthe magnetic trap between the first and second mass analyzers multipletimes.

Charged particles (e.g., ions and electrons) may be manipulated duringoperation of the mass spectrometer by modifying the electric and/ormagnetic fields of one or more of the mass analyzers, magnetic trap, or,when present, other elements of the mass spectrometer. Such manipulationmay be associated with injecting, trapping, sorting, or ejecting ionsfrom the first or second mass analyzers, reversing the ion flow fromdownstream to upstream and from upstream to downstream (e.g., to passions through the magnetic trap multiple times), and/or injecting,trapping, or ejecting electrons from the magnetic trap. Modification ofthe electric and/or magnetic fields of one or more of the mass analyzersor magnetic trap in order to manipulate charged particles in the massspectrometer will depend on the specific mass analyzers and magnetictrap being used with the mass spectrometer as well as the specificarrangement of the mass analyzers, the magnetic trap, and any otherelements of the mass spectrometer.

The mass spectrometer also typically includes an electron source (whenperforming electron capture dissociation) or a positron source (whenperforming positron capture dissociation), although the electron orpositron source may also be external to (i.e., not a part of) the massspectrometer. Whether part of the mass spectrometer or not, the electron(or positron) source is positioned with respect to the magnetic trapsuch that electrons (or positrons) may be supplied to the magnetic trapwhen desired. The electron (or positron) source may be positioned insideor outside of the magnetic trap. Examples of electron sources include,but are not limited to, a thermal electron source (e.g., a tungstenfilament) that may or may not be covered with a substance that providesa low work function (e.g., barium oxide (BaO)). In one embodiment, theelectron source is a mesh electron source that allows the passage ofions through the mesh. Examples of positron sources include, but are notlimited to, radioactive sources such as, for example, ²²Na isotope withthermalizers.

The first and second mass analyzers may be different types of massanalyzers or the same type of mass analyzer. For example, the first massanalyzer could be a quadrupole ion trap and the second mass analyzercould be a quadrupole mass filter, or both the first mass analyzer andthe second mass analyzer could be quadrupole ion traps. The first massanalyzer and the second mass analyzer may be operated to sort, guide,trap, etc. ions in a broad mass-to-charge ratio (m/z) range or a narrowm/z range. In addition, one or more of the first mass analyzer, themagnetic trap, and the second mass analyzer may be positioned within oneor more enclosures with pumps to provide operating conditions withreduced pressure (e.g., a vacuum). Various embodiments using differenttypes of mass analyzers are explained below.

The present invention also includes methods of performing tandem massspectrometry using a mass spectrometer as described above comprising afirst mass analyzer, a magnetic trap, and a second mass analyzer. Ionsare generated using an ion source and are injected into the first massanalyzer. Parent ions to be subjected to electron (or positron) capturedissociation are selected using the first mass analyzer. The parent ionsare subjected to electron (or positron) capture dissociation to produceproduct ions by injecting the parent ions into the magnetic trap andallowing the parent ions to react with electrons (or positrons) trappedin the magnetic trap. The electrons (or positrons) are preferablytrapped in the magnetic trap before the parent ions are injected intothe magnetic trap, but may be trapped in the magnetic trap anytimebefore or during injection of the parent ions into the magnetic trap.The electrons (or positrons) may also be trapped in the magnetic trapbefore, during, or after injection of ions from the ion source into thefirst mass analyzer. After electron (or positron) capture dissociationproduces product ions from at least some of the parent ions, the productions are ejected from the magnetic trap into the second mass analyzer,and the product ions are detected using the second mass analyzer oranother mass analyzer that is part of the mass spectrometer and thatincludes a detector. As mentioned above, the charged particles (i.e.,ions and electrons) are manipulated during the method using appropriatevoltages and magnetic fields to the mass analyzers and magnetic trap.

Illustrative Embodiments of Mass Spectrometer Having a Magnetic Trap

Various embodiments of a mass spectrometer comprising a first massanalyzer, a magnetic trap, and a second mass analyzer are possible. Asstated above, the first and second mass analyzers may be different typesof mass analyzers or the same type of mass analyzer. Three illustrativeembodiments are described below with respect to electron capturedissociation and are intended to be non-limiting.

Embodiment of FIG. 1

FIG. 1 illustrates one embodiment of a mass spectrometer 10 according tothe present invention. The mass spectrometer 10 includes a first linearquadrupole 12 as a first mass analyzer, a magnetic trap 14 (which may bean ideal Penning trap), a second linear quadrupole 16 as a second massanalyzer, a first ion gate 18, a second ion gate 20, and an ion source22.

The magnetic trap 14 includes end-cap electrodes 24, 26 and ringelectrode 28. The end-cap electrodes 24, 26 are magnets and are used asthe source of a magnetic field (B). The end-cap electrodes 24, 26 arealso used, along with the ring electrode 28, as electrodes to generate aquadrupole electric field (a static voltage is applied between theend-cap electrodes 24, 26 and the ring electrode 28).

As illustrated in the figure, the first mass analyzer 12, the magnetictrap 14, and the second mass analyzer 16 are arranged coaxially alongthe axis of the center of the quadrupoles and the center of the openingsof the end-cap electrodes of the magnetic trap 14. The arrows in thefigure illustrate the typical direction of ions through the massspectrometer 10.

In operation of the mass spectrometer 10 of FIG. 1, ions are produced byion source 22 and are injected through ion gate 18 into linearquadrupole 12. The linear quadrupole 12 is used to select parent ions 30in a specified m/z range. The parent ions 30 are injected from thelinear quadrupole 12 into the magnetic trap 14, which contains trappedelectrons 32. The electrons 32 are trapped before injection of theparent ions into the magnetic trap 14. At least some of the parent ions30 react with the electrons 32 and undergo electron capture dissociationto produce product ions 34. The product ions 34 and any remaining parentions are ejected from magnetic trap 14 into linear quadrupole 16.

The linear quadrupoles 12, 16 may be linear radio-frequency quadrupolesand may be operated as linear quadrupole mass filters or linearquadrupole ion traps, and appropriate voltages may be applied to operatethe mass spectrometer 10 accordingly. Also, the voltages of the linearquadrupoles 12, 16, the ion gates 18, 22, and/or the magnetic trap 14may be modified during operation of the mass spectrometer 10 tomanipulate the ions or electrons.

In one more specific embodiment of the mass spectrometer 10 of FIG. 1,the first linear quadrupole 12 could be operated as a quadrupole massfilter and the second linear quadrupole 16 could be operated as a linearquadrupole ion trap. In such an embodiment, the quadrupole mass filtercould be used to select parent ions having a specified m/z range and thequadrupole ion trap 16 could be used to trap product ions within aspecified m/z range. The parent ions passing through the magnetic trap14 without reacting with the electrons 32 could be injected back intothe magnetic trap 14 for fragmentation using electron capturedissociation, and parent and/or product ions passing into the first massanalyzer could be again passed through the magnetic trap 14 and into theion trap 16. During such a process, the ion gates 18, 20 could be usedto generate a potential to trap parent and product ions within the massspectrometer 10. The product ions 34 could eventually be detected by asuitable detector to produce a mass spectrum.

Embodiment of FIG. 2

FIG. 2 illustrates another embodiment of a mass spectrometer 100according to the present invention. The mass spectrometer 100 includes alinear radio frequency quadrupole ion trap 110 as a first mass analyzer,a magnetic trap 120, a linear radio frequency quadrupole mass filter 130as a second mass analyzer, ion gates 140, 145, an ion source 150, anelectron source 155, and a detector 160. As shown in the figure, the iontrap 110, the magnetic trap 120, and the quadrupole mass filter 130 arearranged coaxially.

The magnetic trap 120 includes permanent magnets 170 and a ringelectrode 180 in the shape of a cylinder. The magnetic trap 120 alsoincludes a magnetic flux return yoke, which is not shown in the figure.The magnets 170 are used as the source of a magnetic field and are used,along with the ring electrode 120, as electrodes to generate aquadrupole electric field. As shown in the figure, a static voltage(i.e., V₀) is applied between the magnets and the ring electrode. Thedistance between the two magnets is preferably √{square root over(2)}r₀, which will provide a quadrupole field inside the trap, asillustrated by the electric potential lines 190 shown in the figure. Theelectron source 155 shown beside one of the magnets 170 in FIG. 2 couldbe a thermal electron source such as, for example, a tungsten filament.The electron energy could be controlled by the potential of the filament(i.e., V_(f)).

The first mass analyzer 110 is a linear radio frequency quadrupole iontrap made of four cylindrical rods. A static voltage V₁ and a radiofrequency voltage V_(rf1) with a frequency of Ω₁ are applied to thefirst mass analyzer 110 to establish a quadrupole electric field. Thesecond mass analyzer 130 is a linear quadrupole mass filter also made offour cylindrical rods. A static voltage V₂ and a radio frequency voltageV_(rf2) with a frequency of Ω₂ are applied to the second mass analyzer130 to establish a quadrupole electric field. The quadrupole fields ofthe mass analyzers 110, 130 are used to radially (i.e., in the x and ydirections) confine ions of a selected m/z range within the massanalyzers. Static voltage V_(a) is applied to control the width of theselected m/z range. The linear quadrupole ion trap 110 also confinesions axially (i.e., along the z direction) using static voltages V₃ andV₅ applied to ion gate 140 and the end-cap electrodes 170, respectively.

In operation of the mass spectrometer of FIG. 2, ions are produced byion source 150 and enter the linear radio frequency quadrupole ion trap110 through ion gate 140. The ions are trapped in the ion trap 110 bythe axial confining potential created by static voltages V₃ and V₅ andby the radial confining potential created by voltages V₁ and V_(rf1).The ion trap 110 may be used to select parent ions within a specifiedm/z range. The parent ions are injected into the magnetic trap 120,which contains trapped electrons from electron source 155.

The electrons in the magnetic trap 120 are trapped prior to injection ofthe parent ions into the magnetic trap 120. The electrons are confinedaxially by the static potential created by the application of V₀ betweenthe end-cap electrodes 170 and the ring electrode 180 and are confinedradially by the magnetic field (B) created between the two end-capmagnets 170.

At least some of the parent ions react with the trapped electrons in themagnetic trap 120 and are dissociated into product ions via electroncapture dissociation. The product ions and any remaining parent ions areejected from the magnetic trap 120 into the quadrupole mass filter 130,which may be used to select ions in a specified m/z range and guidethose ions toward the static voltage V₄ of ion gate 145. The ions passthrough the ion gate 145 to detector 160 where the ions are detected anda signal 195 is generated to produce a mass spectrum (not shown).

In one particular embodiment of the mass spectrometer 100 shown in FIG.2, the magnetic trap 120 has a ring electrode 180 in the shape of acylinder with an internal radius (i.e., r₀) of 21.3 mm and end-capelectrodes 170 that are permanent magnets with 1.3 T (e.g., NEO-MAX,Sumitomo Special Metals). The linear radio frequency quadrupole ion trap110 may be made from four cylindrical rods with a diameter of 15.4 mmand a length of 70 mm, with the distance between the center axis to arod surface being 6.7 mm. The linear radio frequency quadrupole massfilter 130 could be made from four cylindrical rods with a diameter of15.4 mm and a length of 224 mm, with the distance between the centeraxis to a rod surface being 6.7 mm. In such an embodiment, an RF voltagewith a frequency of 1.3 MHz could be applied to the linear radiofrequency quadrupole ion trap 110 and a RF voltage with a frequency of1.0 MHz could be applied to the linear radio frequency quadrupole massfilter 130.

Embodiment of FIG. 3

FIG. 3 illustrates another embodiment of a mass spectrometer accordingto the present invention. The mass spectrometer 200 includes anionization source 205, a linear quadrupole mass filter 210, a Penningtrap 220, an electron source 225, a linear quadrupole ion trap 230, agate 235, an ion guide 240, a second gate 245, and a time-of-flight massanalyzer 250. The mass spectrometer 200 includes a pump 260 foroperating the quadrupole mass filter 210, the Penning trap 220, thelinear quadrupole ion trap 230, and the ion guide 240 under reducedpressure (e.g., in a vacuum) in enclosure 262. The mass spectrometer 200also includes a pump 270 for operating the time-of-flight analyzer 250at a reduced pressure (e.g., in a vacuum) in enclosure 272. The magneticion trap 220 includes magnetic end-cap electrodes 215 and ring electrode217. The time-of-flight mass analyzer 250 includes lens 280, pusher 282,reflectron 284, and microchannel plate detector 286. Arrows in FIG. 3show the direction of ions into the quadrupole mass filter 210 as wellas from ion guide 240 through the time-of-flight mass analyzer 250.

In operation of the mass spectrometer of FIG. 3, ions are produced byion source 205 and are injected into the linear quadrupole mass filter210. The quadrupole mass filter 210 may be used to select parent ionswithin a specified m/z range. The parent ions are injected into themagnetic trap 220, which contains trapped electrons from electron source225. The electrons in the magnetic trap 220 are trapped prior toinjection of the parent ions into the magnetic trap 220. At least someof the parent ions react with the trapped electrons in the magnetic trap220 and are dissociated into product ions via electron capturedissociation. The product ions and any remaining parent ions are ejectedfrom the magnetic trap 220 into the linear quadrupole ion trap 230,which includes gates 235 and 245. The selected ions pass through the ionguide 240 to the time-of-flight mass analyzer 250, where the ions aredetected by the microchannel plate detector 286.

Electron Capture Dissociation in an Ideal Penning Trap

In order to further explain the present invention, various aspects ofelectron capture dissociation in an ideal Penning trap are theoreticallydescribed below.

Electron capture dissociation can be represented by the followingequation (1),M ^(+Q) +e ⁻ =m ^(+q)+(M−m)^(Q−q−1) +K _(p) +k _(p)  (1)where a parent ion having a mass of M and charge of +Q reacts with anelectron having a mass of m_(e) and a charge of −1. Product ions areproduced that have masses of m and (M−m) and charges of +q and Q−q−1,respectively. The reaction releases energy K_(p)+k_(p). K_(p) and k_(p)represent the kinetic energy of the ion m^(+q) and the ion(M−m)^(Q−q−1), respectively, at an infinite distance from each other.Cross Section of Electron Capture Dissociation

The typical reaction cross section of electron capture dissociation(i.e., σ_(ECD)) is 10⁻¹⁵ m² for electrons with ˜1 eV (see, e.g., Zubarevet al., Electron Capture Dissociation for Structural Characterization ofMultiply Charged Protein Cations, Anal. Chem., 72, 563–573 (2000)).Using the cross section, reaction probability (i.e., r_(ECD)) is givenby the following equation (2)r _(ECD)=1−exp(−σ_(ECD) ρΔtv _(e))  (2)where ρ is the density of the electrons, v_(e) is the velocity ofelectrons, and Δt is the interaction time (i.e., the period that aparent ion locates between one end cap and another end cap). In derivingequation (2), it was assumed that the velocity of the electrons is muchlarger than the velocity of the parent ions. As illustrated by equation(2), a large electron density and a large interaction time are requiredto obtain a large reaction probability.

The reaction energy of electron capture dissociation (i.e., K_(react))does not depend on the kinetic energy of the parent ions (i.e., K) inthe laboratory system. When the kinetic energy of a parent ion (i.e., K)and the kinetic energy of the electron (i.e., K_(e)) are approximatelyequal (i.e., when K˜K_(e)), the reaction energy (i.e., K_(react)) isequal to the electron kinetic energy as shown by the followingapproximation,

$\begin{matrix}{K_{react} = {K_{e} - {2{{\left. \sqrt{\frac{m_{e}}{m}K_{e}K} \right.\sim K_{e}}.}}}} & (3)\end{matrix}$This means that the reaction energy (i.e., K_(react)) should be able tobe controlled by the kinetic energy (or temperature) of the electronsused in the electron capture dissociation reaction.Equation of Motions

Equations (4), (5), and (6) below describe the motion of a chargedparticle with mass of m and charge of q in an ideal Penning trap (i.e.,in a Penning trap that has a uniform magnetic field applied to the zdirection, (0, 0, B), and an ideal quadrupole DC potential,ψ=V₀(x²+y²−2z²)/2r₀ ²). The equations can be used to describe the motionof electrons as well as parent and product ions in an ideal Penningtrap.

$\begin{matrix}{{m\frac{\mathbb{d}^{2}}{\mathbb{d}t^{2}}x} = {{{qv}_{y}B} - {{qV}_{0}\;\frac{x}{r_{0}^{2}}}}} & (4)\end{matrix}$

$\begin{matrix}{{m\frac{\mathbb{d}^{2}}{\mathbb{d}t^{2}}y} = {{{- {qv}_{x}}B} - {{qV}_{0}\;\frac{y}{r_{0}^{2}}}}} & (5)\end{matrix}$

$\begin{matrix}{{m\frac{\mathbb{d}^{2}}{\mathbb{d}t^{2}}z} = {{qV}_{0}\;\frac{2z}{r_{0}^{2}}}} & (6)\end{matrix}$where r₀ represents the central internal radius of the ring electrode, Brepresents the magnetic field strength, (v_(x),v_(y),v_(z)) representsthe velocity of the charged particle and x, y, and z represent theposition of the charged particle in the x, y, and z directions, with thecoordinate z=0, x=0, y=0 being at the center of the Penning trap alongthe z axis formed by the apertures in the end-caps.Electron storage

The maximum density of electrons in the Penning trap may be estimatedwhen the DC voltage (i.e., V₀) of the Penning trap satisfies thestability condition of the Penning trap (i.e., the magnetron motionstability), which is given by Equation 7:

$\begin{matrix}{V_{0} \leq \frac{{eB}^{2}}{4m_{e}r_{0}^{2}}} & (7)\end{matrix}$where e and m_(e) represent the charge and the mass, respectively, of anelectron. This condition should be satisfied under typical operatingconditions. For example, this condition would be satisfied if V₀=10 V,r₀=21.3 mm, and B=1.3 T, because 10 V is smaller than the right handside of equation (7), which is ˜1 kV.

If the stability condition is satisfied, the maximum electron density inthe Penning trap (i.e., ρ) is given by the lower value of the followingtwo categories: (1) Brillouin condition, which is a balance of therepulsive Coulomb force between charges and a rotating force in themagnetic field and is represented by Equation (8) below and (2) thespace charge limit density in a confinement potential (when it isassumed that a space charge is an infinitely long cylinder of uniformdensity), which is represented by equation (9) below:

$\begin{matrix}{\rho = {\text{∈}_{0}\frac{{eB}^{2}}{2m_{e}}}} & (8)\end{matrix}$where ε₀ is the dielectric constant of vacuum,

$\begin{matrix}{\rho = {\text{2∈}_{0}{\frac{V_{0}}{r_{0}^{2}}.}}} & (9)\end{matrix}$When V₀=10 V, r₀=21.3 mm, and B=1.3 T, the maximum density is given byequation (9) because the value of equation (9) is much smaller than thevalue given by the Brillouin condition, equation (8).

FIG. 4 includes a plot of maximum electron density in a Penning trapunder varying voltages. The maximum electron density is shown by thethick line in the FIG. 4 and was calculated using Equation (9). As shownin the figure, the maximum electron density depends linearly on V₀.

Interaction Time

The reaction efficiency of electron capture dissociation depends on theinteraction time (i.e., Δt) of the parent ion, which is obtained bysolving the equation of motion, equation (6), and is given below asEquation (10):

$\begin{matrix}{{\Delta\; t} = {\sqrt{\frac{2{mr}_{0}^{2}}{{qV}_{0}}}\sinh^{- 1}\sqrt{\frac{{qV}_{0}}{2\;\Delta\; K}}}} & (10)\end{matrix}$where ΔK (i.e., the kinetic energy of the parent ion at z=0) is equal toK_(i)−V₀/2, with K_(i) being the kinetic energy of the parent ion at theend cap electrodes.

In the estimation of the interaction time in equation (10), theexistence of electrons in the Penning trap was ignored. When electronsare stored in the Penning trap, the static potential along the z axis(i.e., the axis between the center of the apertures in the end-capelectrodes) is lowered by the space charge of the electrons, whichresults in a larger interaction time than the above estimation.

As shown in FIG. 4, equation (10) was used to plot Penning trap DCvoltage (i.e., V₀) versus interaction time of a parent ion with amass-to-charge ratio (i.e., m/z) of 1000 Da (represented by the thinlines on FIG. 4). The following values were chosen for ΔK, with eachvalue shown next to the appropriate line in FIG. 4: 0.03 eV, 0.1 eV, 0.3eV, 1 eV, 3 eV, and 10 eV. As illustrated in FIG. 4, a relatively smallV₀ and small ΔK give a relatively large interaction time.

Reaction Probability

FIG. 5 shows a plot of reaction probability calculated using equation(2). In calculating the graph, the mass-to-charge ratio of the parentions was fixed to 1000 Da and the following values were used for thekinetic energy of the parent ions at z=0 (i.e., ΔK): 0.03 eV, 0.1 eV,0.3 eV, 1 eV, 3 eV, and 10 eV. In addition, the kinetic energy of theelectrons was fixed to 1 eV.

As shown in FIG. 5, in order to obtain a large reaction probability, V₀should be large and ΔK should be small. When ΔK=0.1 eV and V₀=20 eV, thereaction probability is about 20%.

As discussed above, parent ions could be passed through the electronstrapped in the Penning trap several times in order to increase thereaction probability.

Ejection of Product Ions

The ejection efficiencies of product ions of varying mass-to-chargeratios (m/z) from the magnetic trap were calculated by Monte Carlosimulation using the equations of motion (i.e., equations (4)–(6)). Theelectron capture dissociation reaction of the parent ion was set tooccur on the z axis. The reaction point on the z axis (i.e., z₀) and thevelocity (i.e., v₀) of a parent ion are given by the solution of theequation of motion (i.e., equation (6)) and are shown below as equations(11) and (12), respectively:

$\begin{matrix}{z_{0} = {\sqrt{\frac{\Delta\; K}{{qV}_{0}}}r_{0}\sinh\sqrt{\frac{2{qV}_{0}}{{mr}_{0}^{2}}}t}} & (11)\end{matrix}$

$\begin{matrix}{v_{0} = {\sqrt{\frac{2\Delta\; K}{m}}\cosh\sqrt{\frac{2{qV}_{0}}{{mr}_{0}^{2}}}t}} & (12)\end{matrix}$where t is given randomly with a constraint of [z₀]<r₀/√{square rootover (2)}. The product ion was approximated to have kinetic energy K_(p)plus kinetic energy of the parent ion that reacts with the electron. Inorder to account for the kinetic energy of the parent ion, a velocitywith a speed √{square root over (2K_(p)/m)} and a spherically randomdirection was added to the velocity of the parent ion (i.e., v₀). Whenthe product ion reaches one of the holes on the two end cap electrodes,the ion was judged to be ejected from the magnetic trap. The ejectionefficiency was defined as a ratio of ejected events when 10,000 eventswere shot for Monte Carlo simulation.

FIG. 6 illustrates a graph of kinetic energy of product ions (i.e.,K_(p)) versus ejection efficiency of the product ions from the Penningtrap as calculated using Monte Carlo simulation. The kinetic energy ofthe parent ions at z=0 (i.e., ΔK) was fixed to 0.1 [eV] and the Penningtrap static voltage (i.e., V₀) was fixed to 20 Volts. As discussedabove, the kinetic energy of the product ions (i.e., K_(p)) depends onthe reaction.

When there is no electromagnetic field in the Penning trap (i.e., B=0and V₀=0), the ejection efficiency of the product ions is given by thesolid angle of the hole. The thick dashed line in FIG. 6 representsejection efficiency of product ions when there is no field in thePenning trap.

As shown by the thick solid line in FIG. 6, applying a static DC voltageof 20 V to the Penning trap (i.e., V₀) in the absence of a magneticfield (i.e., B=0) enhances the ejection efficiency of product ions whenK_(p) is small as compared to the ejection efficiency of product ions inno field at all. This is because the quadrupole static field focuses theions in the radial direction as well as forces the ions along the zaxis.

When the Penning trap has no magnetic field (i.e., B=0), the ejectionefficiency of product ions is less dependent on the mass of the productions than when there is a magnetic field present in the Penning trap.

As shown in FIG. 6, the thin lines represent the mass dependence of theejection efficiencies when B=1.3 T and V₀=20 V for product ions havingmasses of 30, 100, 300, and 1000 Da. The magnetic field enhances theejection efficiency because the magnetic field traps the ions radiallyalong the z direction and the trajectory of the ions are spiral alongthe z direction. As can be seen in the figure, the magnetic field ismore effective for ions with less mass. This is because the cyclotronradius of product ions is inversely proportional to the mass-to-chargeratio. Therefore, stronger magnetic fields will provide higher ejectionefficiencies of product ions.

The mass spectrometer described above may also include additionaltrapping electrodes adjacent to the ring electrode of the magnetic trapeither inside of the end-cap electrodes of the Penning trap (such thatthe additional trapping electrodes are between the end-cap electrodesand the ring electrode) or outside of the end-cap electrodes of thePenning trap (such that each end-cap electrode is between eachadditional trapping electrode and the ring electrode). Such additionaltrapping electrodes could be used, in conjunction with the magnetictrap, to trap both electrons and positively charged ions in the magnetictrap for electron capture dissociation or to trap both positrons andnegatively charged ions in the magnetic trap for positron capturedissociation. After electron (or positron) capture dissociation of theions, appropriate voltages to the magnetic trap, the additional trappingelectrodes, and/or other elements of the mass spectrometer could be usedto manipulate the product ions (e.g., to eject the product ions from themagnetic trap and into the second mass analyzer). The additionaltrapping electrodes could be in any form and could be, for example,plate electrodes with apertures or mesh electrodes.

When the mass spectrometer includes additional trapping electrodes suchthat oppositely charged particles (e.g., electrons andpositively-charged ions) may be trapped in the Penning trap, the ions tobe subjected to electron (or positron) capture dissociation may beinjected into the magnetic trap either before, after, or during loadingof electrons (or positrons) into the magnetic trap. After electron (orpositron) capture dissociation, appropriate voltages may be applied tothe additional trapping electrodes, the magnetic trap, and/or the firstor second mass analyzers ion order to eject the product ions from themagnetic trap into either the first or the second mass analyzer. Theproduct ions may then be analyzed in an area separate from the electron(or positron) capture dissociation cell (e.g., in order to produce atandem mass spectrum).

FIG. 7 illustrates a mass spectrometer 300 with additional trappingelectrodes 310. The mass spectrometer 300 includes an ion source 305, afirst mass analyzer 315 (e.g., a quadrupole mass analyzer), an ion gate320, a magnetic trap 325 with magnetic end-cap electrodes 327 and a ringelectrode 329, mesh electrodes 310, an electron source 330, another iongate 333, a second mass analyzer 335 (e.g., a quadrupole mass analyzer),and a third mass analyzer 340 with a detector (e.g., a time-of-flightmass analyzer with a detector). As illustrated in FIG. 7, the magnetictrap 325 could be used in conjunction with the mesh trapping electrodes310 to trap both electrons 345 and positive ions 350. FIG. 7 includes agraph of a possible electric potential along the z axis when bothelectrons 345 and positive ions 350 are confined in the magnetic trap325 using the magnetic trap 325 and the additional trapping electrodes310.

In operation of the mass spectrometer 300 of FIG. 7, ions are producedby ion source 305 and are injected into the first mass analyzer 315,which is used to select parent ions in a specified m/z range. The parentions are injected into the magnetic trap 325 and confined. Eitherbefore, after, or during injection of the parent ions into the magnetictrap 325, electrons generated by electron source 330 are confined in themagnetic trap 325. After at least some of the parent ions react with theelectrons 345 and undergo electron capture dissociation to produceproduct ions, the product ions and any remaining parent ions are ejectedfrom the magnetic trap 325 into the second mass analyzer 335. The secondmass analyzer 335 is used to inject the product ions to the third massanalyzer 340, which is used to produce a mass spectrum of the productions. Although the mass spectrometer 300 is shown and described withrespect to electron capture dissociation, the mass spectrometer couldalso be used for positron capture dissociation by confining bothpositrons and negative ions in magnetic trap 325.

In another aspect of the invention, electron (or positron) capturedissociation may be performed by confining ions to a region within amagnetic trap and passing electrons (or positrons) through the trap.When electron capture dissociation is to be performed, the ions aretypically positive ions, and when positron capture dissociation is to beperformed, the ions are typically negative ions. After electron (orpositron) capture dissociation, the product ions may be ejected to amass analyzer and analyzed outside of the magnetic trap. A massspectrometer comprising a first analyzer, a magnetic trap, and a secondanalyzer as described above could be used for such electron (orpositron) capture dissociation, with appropriate voltages and anappropriate magnetic field applied to the magnetic trap in order to trapions rather than electrons (or positrons). After the ions are trapped inthe magnetic trap, electrons (or positrons) from an appropriate sourceare directed through the magnetic trap (e.g., through one of theapertures of the end-cap electrodes) such that electron (or positron)capture dissociation of at least a some of the ions occurs.

Electron (or positron) capture dissociation in such a manner alsoprovides methods of performing tandem mass spectrometry using a massspectrometer as described above comprising a first mass analyzer, amagnet trap, and a second mass analyzer. Ions are generated using an ionsource and are injected into the first mass analyzer. Parent ions to besubjected to electron (or positron) capture dissociation are selectedusing the first mass analyzer and are then injected into and confinedwithin the magnetic trap. Electrons (or positrons) are provided (e.g.,by an electron or positron source) and are injected into the magnetictrap for reaction with the confined ions. Electron (or positron) capturedissociation of at least some of the parent ions produces product ions,which are ejected from the trap into the second mass analyzer. Theproduct ions are detected and a mass spectrum may be produced. Asmentioned above, the charged particles (i.e., ions and electrons) aremanipulated during the method using appropriate voltages and magneticfields to the mass analyzers and magnetic trap.

In another aspect of the invention, electron (or positron) capturedissociation may be performed by passing ions through a regioncontaining electrons (or positrons) (i.e., an electron (or positron)region). The region containing electrons (or positrons) is preferably afield-free region (i.e., a region with no electric or magnetic fieldsfor trapping electrons or ions). When electron capture dissociation isto be performed, the ions are typically positive ions, and when positroncapture dissociation is to be performed, the ions are typically negativeions. In addition, the ions are preferably multiply charged ions (i.e.,the ions preferably have a charge state of 2 or more).

A mass spectrometer capable of performing electron (or positron) capturedissociation using such a method comprises a first mass analyzer, anelectron (or positron) source, an electron (or positron) region (e.g., afield-free region), and a second mass analyzer. The mass spectrometerpreferably includes means for creating a field-free region in order tocreate a field-free region for electrons (or positrons) from theelectron (or positron) source. For example, the mass spectrometer mayinclude two grounded electrodes in order to provide a field free regionbetween the grounded electrodes. Such grounded electrodes could be, forexample, plates with apertures that allow ions to pass through thefield-free region or could be mesh electrodes that allow the passage ofions.

The first mass analyzer, the electron (or positron) source, the electron(or positron) region (e.g., the field-free region), and the second massanalyzer are arranged such that ions may move from the first massanalyzer through the region for containing electrons (or positrons)(e.g., the field-free region) to the second mass analyzer. That is, thefirst mass analyzer, the region for containing electrons (or positrons)(e.g., the field-free region), and the second mass analyzer are arrangedin series (linear or otherwise). The electron (or positron) source ispositioned such that electrons (or positrons) may be supplied to theelectron (or positron) region (e.g., the field-free region) whendesired.

The mass spectrometer may consist only of the first mass analyzer, theelectron (or positron) source, the region for containing electrons (orpositrons), and the second mass analyzer, or may include other elements.In one embodiment, the mass spectrometer does not include a magnetictrap.

The electron (or positron) source may be inside or outside of theelectron (or positron) region as long as electrons (or positrons) forelectron (or positron) capture dissociation may be supplied to theregion when desired. Examples of electron sources include, but are notlimited to, a thermal electron source (e.g., a tungsten filament ormesh) that may or may not be covered with a substance that provides alow work function (e.g., barium oxide (BaO)). In one embodiment, theelectron source is a mesh electron source that allows the passage ofions through the mesh.

The mass spectrometer typically includes an ion source to supply ions tothe first mass analyzer, although the ion source may be external to(i.e., not a part of) the mass spectrometer. Ions may be supplied usingion sources that use electrospray ionization (ESI), nanoelectrosprayionization (nESI), matrix assisted laser desorption ionization (MALDI),electron impact ionization (EI) or any other method for producing ions.The ion flow in the mass spectrometer is typically from an ion source tothe first mass analyzer, from the first mass analyzer through theelectron (or positron) region (e.g., a field free region) containingelectrons (or positrons) to the second mass analyzer.

The first and second mass analyzers may be different types of massanalyzers or the same type of mass analyzer. For example, the first massanalyzer could be a quadrupole ion trap and the second mass analyzercould be a quadrupole mass filter, or both the first mass analyzer andthe second mass analyzer could be quadrupole ion traps. The first massanalyzer and the second mass analyzer could be operated to sort, guide,trap, etc. ions in a broad mass-to-charge ratio (m/z) range or a narrowm/z range. In addition, one or more of the first mass analyzer, theelectron (or positron) region (e.g., the field-free region), and thesecond mass analyzer may be positioned within one or more enclosureswith pumps to provide operating conditions with reduced pressure (e.g.,a vacuum).

Charged particles (e.g., ions) may be manipulated during operation ofthe mass spectrometer by modifying the electric fields of one or more ofthe mass analyzers or other elements of the mass spectrometer. Suchmanipulation may be associated with injecting, trapping, sorting, orejecting ions from the first or second mass analyzers and/or reversingthe ion flow from downstream to upstream and from upstream to downstream(e.g., to pass ions through the electron (or positron) region multipletimes). Modification of the electric fields of one or more of the massanalyzers in order to manipulate charged particles in the massspectrometer will depend on the specific mass analyzers being used withthe mass spectrometer as well as the specific arrangement of the massanalyzers and any other elements of the mass spectrometer.

The present invention also includes methods of performing tandem massspectrometry using a mass spectrometer as described above comprising afirst mass analyzer, an electron (or positron) source, an electron (orpositron) region (e.g., the field-free region), and a second massanalyzer. Ions are generated using an ion source and are injected intothe first mass analyzer. Parent ions to be subjected to electron (orpositron) capture dissociation are selected in the first massspectrometer and are injected into the region containing electrons (orpositrons) (e.g., a field-free region containing electrons orpositrons). At least some of the parent ions react with the electrons(or positrons) in the electron (or positron) region and are dissociatedinto product ions via electron (or positron) capture dissociation. Atleast some of the product ions pass into the second mass analyzer andmay be detected using a detector of the second (or another) massanalyzer. When the electron (or positron) region is a field-free region(i.e., when the mass spectrometer further comprises means for creating afield free region between the first and second mass analyzers), theparent ions must have sufficient kinetic energy to enter the field freeregion and react with the electrons (or positrons) therein, and theproduct ions must have sufficient kinetic energy formed by electroncapture dissociation to reach the second mass analyzer once they areformed.

Examples of mass spectrometers capable of performing electron (orpositron) capture dissociation (and tandem mass spectrometry) by passingions through a field-free region are illustrated in FIGS. 8 and 9. Themass spectrometer 400 illustrated in FIG. 8 includes an ion source 405,a first ion gate 410, a first mass analyzer 415, mesh electrodes 420 and430, an electron (or positron) source 435, a field-free region 425, asecond mass analyzer 440, a second ion gate 445, and a third massanalyzer 450 with a detector. In operation of the mass spectrometer 400,ions generated by ion source 405 are injected through ion gate 410 intothe first mass analyzer 415, where parent ions 455 having a specifiedm/z range are selected for electron (or positron) capture dissociation.The mesh electrodes 420 and 430 are used to create a field-free region425 (e.g., by grounding the mesh electrodes 420 and 430). Electrons (orpositrons) 437 from the electron (or positron) source 435 are passedthrough the field-free region 425. The parent ions 455 selected by thefirst mass analyzer are passed through the field-free region 425 forreaction with the electrons (or positrons) 437. At least some of theparent ions 455 react with the electrons (or positrons) 437 in thefield-free region 425 and are dissociated into product ions via electron(or positron) capture dissociation. At least some of the product ionspass into the second mass analyzer 440, which is used to select and/orguide product ions 460. The product ions 460 are passed through ion gate445 and are analyzed by the third mass analyzer 450 to produce a massspectrum (not shown). The movement of the ions through the massspectrometer is shown by the horizontal arrows along the z axis.

FIG. 9 illustrates another mass spectrometer 500 capable of performingelectron capture dissociation (and tandem mass spectrometry) by passingions through a field-free region. The mass spectrometer 500 includes anion source 505, a first ion gate 510, a first mass analyzer 515, meshelectrodes 520 and 530, a mesh electron source 525 (e.g., a tungstenmesh plated with BaO), a field-free region 535, a second mass analyzer545, a second ion gate 550, and a third mass analyzer 560 with adetector. In operation of the mass spectrometer 500, ions generated bythe ion source 505 are injected through ion gate 510 into the first massanalyzer 515, where parent ions 570 having a specified m/z range areselected for electron capture dissociation. The mesh electrodes 520 and530 are used to create a field-free region 535. Electrons 540 aregenerated by the mesh electron source 525 in the field-free region 535.The parent ions 570 selected by the first mass analyzer 515 are passedthrough the field-free region 535 for reaction with the electrons 540.At least some of the parent ions 570 react with the electrons 540 in thefield-free region 535 and are dissociated into product ions via electroncapture dissociation. At least some of the product ions pass into thesecond mass analyzer 545, which is used to select and/or guide productions 575. The product ions 575 are passed through ion gate 550 into thethird mass analyzer 560 for analysis and production of a mass spectrum.The movement of the ions through the mass spectrometer 500 is shown bythe horizontal arrows along the z axis.

While the invention has been described in detail and with reference tospecific embodiments thereof, it will be apparent to one skilled in theart that various changes and modifications can be made without departingfrom the spirit and scope of the invention.

1. A mass spectrometer comprising: a first mass analyzer; a magnetictrap downstream of the first mass analyzer to trap charged particlesusing a static electric field and a static magnetic field, wherein themagnetic trap has permanent magnet end cap electrodes; a second massanalyzer downstream of the magnetic trap; and an electron or positronsource positioned such that electrons or positrons may be supplied tothe magnetic trap.
 2. The mass spectrometer of claim 1 wherein one orboth of the first and second mass analyzers include a detector.
 3. Themass spectrometer of claim 1 further comprising an ion source.
 4. Themass spectrometer of claim 3 wherein the ion source is an electrosprayionization source, a nanoelectrospray ionization source, or a matrixassisted laser desorption ionization source.
 5. The mass spectrometer ofclaim 1 wherein the first mass analyzer is a time-of-flight massanalyzer, a quadrupole mass filter, or a quadrupole ion trap.
 6. Themass spectrometer of claim 1 wherein the first mass analyzer is a linearradio frequency quadrupole mass analyzer.
 7. The mass spectrometer ofclaim 6 wherein the linear radio frequency quadrupole mass analyzer is aquadrupole mass filter or a quadrupole ion trap.
 8. The massspectrometer of claim 1 wherein the second mass analyzer is atime-of-flight mass analyzer, a quadrupole mass filter, or a quadrupoleion trap.
 9. The mass spectrometer of claim 1 wherein the second massanalyzer is a linear radio frequency quadrupole mass analyzer.
 10. Themass spectrometer of claim 9 wherein the linear radio frequencyquadrupole mass analyzer is a quadrupole mass filter or a quadrupole iontrap.
 11. The mass spectrometer of claim 1 wherein the magnetic trap isan ideal Penning trap.
 12. The mass spectrometer of claim 1 wherein thefirst mass analyzer is a linear radio frequency quadrupole mass analyzerand the second mass analyzer is a linear radio frequency quadrupole massanalyzer.
 13. The mass spectrometer of claim 1 further comprising athird mass analyzer downstream of the second mass analyzer.
 14. The massspectrometer of claim 13 wherein the third mass analyzer is atime-of-flight mass analyzer.
 15. The mass spectrometer of claim 1further comprising an ion source and wherein the first mass analyzer isa linear radio frequency quadrupole mass analyzer and the second massanalyzer is a linear radio frequency quadrupole mass analyzer.
 16. Themass spectrometer of claim 15 further comprising a third mass analyzerdownstream of the second mass analyzer.
 17. The mass spectrometer ofclaim 16 wherein the third mass analyzer is a time-of-flight massanalyzer.
 18. A mass spectrometer of claim 1, wherein the magnetic traphas a magnetic field strength larger than 0.5 Tesla.
 19. The massspectrometer of claim 1, wherein the electron source is selected fromthe group consisting of a thermal and a mesh electron source.
 20. Themass spectrometer of claim 1, wherein the first and second massanalyzers are selected from the group consisting of magnetic sectors,linear and three-dimensional quadrupoles, other multipole analyzers, andtime-of-flight mass analyzers.
 21. The mass spectrometer of claim 1,wherein the magnetic trap further comprises a ring electrode.
 22. Themass spectrometer of claim 1, wherein the magnetic trap has a magneticfield strength of 1.3 T or larger.
 23. A mass spectrometer comprising: afirst mass analyzer; a magnetic trap downstream of the first massanalyzer to trap charged particles using a static electric field and astatic magnetic field, wherein the magnetic trap has permanent magnetend cap electrodes; a second mass analyzer downstream of the magnetictrap; an electron or positron source positioned such that electrons orpositrons may be supplied to the magnetic trap; and two additionaltrapping electrodes, one of the additional trapping electrodespositioned between the first mass analyzer and the magnetic trap and theother additional trapping electrode positioned between the second massanalyzer and the magnetic trap.
 24. A method of performing electroncapture dissociation of ions comprising: (a) generating electrons usingan electron source; (b) confining the electrons to a region within amagnetic trap, wherein the magnetic trap uses a static electric fieldand a static magnetic field to trap charged particles, further whereinthe magnetic trap has permanent magnet end cap electrodes; and (c)injecting positive ions into the magnetic trap such that electroncapture dissociation of at least some of the ions occurs.
 25. A methodof performing positron capture dissociation of ions comprising: (a)generating positrons using a positron source; (b) confining thepositrons to a region within a magnetic trap, wherein the magnetic trapuses a static electric field and a static magnetic field to trap chargedparticles, further wherein the magnetic trap has permanent magnet endcap electrodes; and (c) injecting negative ions into the magnetic trapsuch that positron capture dissociation of at least some of the ionsoccurs.
 26. A method of performing tandem mass spectrometry using a massspectrometer comprising a first mass analyzer, a magnetic trap, and asecond mass analyzer, the method comprising: (a) generating positivesample ions using an ion source; (b) injecting the sample ions into thefirst mass analyzer; (c) using the first mass analyzer, selecting parentions from the sample ions to be subjected to electron capturedissociation; (d) injecting the parent ions into the magnetic trap forreaction with electrons confined in the magnetic trap such that electroncapture dissociation of at least some of the parent ions occurs toproduce product ions, wherein the magnetic trap uses a static electricfield and a static magnetic field to trap charged particles, furtherwherein the magnetic trap has permanent magnet end cap electrodes; (e)ejecting the product ions from the magnetic trap into the second massanalyzer; and (f) detecting the product ions using the second massanalyzer.
 27. The method of claim 26, wherein the first mass analyzercomprises a linear radio frequency quadrupole mass analyzer and thesecond mass analyzer comprises a linear radio frequency quadruple massanalyzer.
 28. A method of performing tandem mass spectrometry using amass spectrometer comprising a first mass analyzer, a magnetic trap, anda second mass analyzer, the method comprising: (a) generating negativesample ions using an ion source; (b) injecting the sample ions into thefirst mass analyzer; (c) using the first mass analyzer, selecting parentions from the sample ions to be subjected to positron capturedissociation; (d) injecting the parent ions into the magnetic trap forreaction with positrons confined in the magnetic trap such that positroncapture dissociation of at least some of the parent ions occurs toproduce product ions, wherein the magnetic trap uses a static electricfield and a static magnetic field to trap charged particles, furtherwherein the magnetic trap has permanent magnet end cap electrodes; (e)ejecting the product ions from the magnetic trap into the second massanalyzer; and (f) detecting the product ions using the second massanalyzer.
 29. The method of claim 28, wherein the first mass analyzercomprises a linear radio frequency quadrupole mass analyzer and thesecond mass analyzer comprises a linear radio frequency quadrupole massanalyzer.
 30. A method of performing tandem mass spectrometry using amass spectrometer comprising a first mass analyzer, a magnetic trap, anda second mass analyzer, the method comprising: (a) generating positivesample ions using an ion source; (b) injecting the sample ions into thefirst mass analyzer; (c) using the first mass analyzer, selecting parentions from the sample ions to be subjected to electron capturedissociation; (d) injecting and confining the parent ions in themagnetic trap, wherein the magnetic trap uses a static electric fieldand a static magnetic field to trap charged particles, further whereinthe magnetic trap has permanent magnet end cap electrodes; (e) injectingelectrons into the magnetic trap for reaction with the confined parentions such that electron capture dissociation of at least some of theparent ions occurs to produce product ions; (f) ejecting the productions from the magnetic trap into the second mass analyzer; and (g)detecting the product ions using the second mass analyzer.
 31. A methodof performing tandem mass spectrometry using a mass spectrometercomprising a first mass analyzer, a magnetic trap, and a second massanalyzer, the method comprising: (a) generating negative sample ionsusing an ion source; (b) injecting the sample ions into the first massanalyzer; (c) using the first mass analyzer, selecting parent ions fromthe sample ions to be subjected to positron capture dissociation; (d)injecting and confining the parent ions in the magnetic trap, whereinthe magnetic trap uses a static electric field and a static magneticfield to trap charged particles, further wherein the magnetic trap haspermanent magnet end cap electrodes; (e) injecting positrons into themagnetic trap for reaction with the confined parent ions such thatpositron capture dissociation of at least some of the parent ions occursto produce product ions; (f) ejecting the product ions from the magnetictrap into the second mass analyzer; and (g) detecting the product ionsusing the second mass analyzer.
 32. A mass spectrometer comprising: afirst mass analyzer; a field-free region downstream from the first massanalyzer; an electron or positron source positioned such that electronsor positrons may be supplied to the field-free region; and a second massanalyzer downstream of the field-free region, wherein the electronsource is a mesh electron source positioned in the field-free region.33. A method of performing tandem mass spectrometry using a massspectrometer comprising a first mass analyzer, a field-free region, anelectron source, and a second mass analyzer, the method comprising: (a)generating positive sample ions using an ion source; (b) injecting thesample ions into the first mass analyzer; (c) using the first massanalyzer, selecting parent ions from the sample ions to be subjected toelectron capture dissociation; (d) providing electrons in the field-freeregion using the electron source; (e) injecting the parent ions into thefield-free region such that electron capture dissociation of at leastsome of the product ions occurs and such that at least some of theproduct ions pass into the second mass analyzer; and (f) detecting theproduct ions using the second mass analyzer, wherein the electron sourceis a mesh electron source positioned in the field-free region.